Protein and peptide folding, misfolding, and non-folding

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Protein and peptide folding, misfolding, and non-folding / edited by Reinhard Schweitzer-Stenner

資料種別:: 図書
出版情報:: Hoboken, N.J. : Wiley, c2012
形態:: xxii, 548 p., [24] p. of plates ; 26 cm
シリーズ名:: Wiley series in protein and peptide science <BB00764902>
著者名:: Schweitzer-Stenner, Reinhard
ISBN:: 9780470591697 [0470591692]
書誌ID:: BB10956193

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注記:

Includes bibliographical references and index

主題:

Peptides; Protein folding

言語:

英語

目次情報:

Introduction to the Wiley Series on Protein and Peptide Science

Preface

Contributors

Introduction

Why Are We Interested in the Unfolded Peptides and Proteins? / Vladimir N. Uversky ; A. Keith Dunker1：

Why Study IDPs? / 1.1：

Lesson 1: Disorderedness Is Encoded in the Amino Acid Sequence and Can Be Predicted / 1.3：

Lesson 2: Disordered Proteins Are Highly Abundant in Nature / 1.4：

Lesson 3: Disordered Proteins Are Globally Heterogeneous / 1.5：

Lesson 4: Hydrodynamic Dimensions of Natively Unfolded Proteins Are Charge Dependent / 1.6：

Lesson 5: Polymer Physics Explains Hydrodynamic Behavior of Disordered Proteins / 1.7：

Lesson 6: Natively Unfolded Proteins Are Pliable and Very Sensitive to Their Environment / 1.8：

Lesson 7: When Bound, Natively Unfolded Proteins Can Gain Unusual Structures / 1.9：

Lesson 8: IDPs Can Form Disordered or Fuzzy Complexes / 1.10：

Lesson 9: Intrinsic Disorder Is Crucial for Recognition, Regulation, and Signaling / 1.11：

Lesson 10: Protein Posttranslational Modifications Occur at Disordered Regions / 1.12：

Lesson 11: Disordered Regions Are Primary Targets for AS / 1.13：

Lesson 12: Disordered Proteins Are Tightly Regulated in the Living Cells / 1.14：

Lesson 13: Natively Unfolded Proteins Are Frequently Associated with Human Diseases / 1.15：

Lesson 14: Natively Unfolded Proteins Are Attractive Drug Targets / 1.16：

Lesson 15: Bright Future of Fuzzy Proteins / 1.17：

Acknowledgments

References

Conformational Analysis of Unfolded States / I：

Exploring the Energy Landscape of Small Peptides and Proteins by Molecular Dynamics Simulations / Gerhard Stock ; Abhinav Jain ; Laura Riccardi ; Phuong H. Nguyen2：

Introduction: Free Energy Landscapes and How to Construct Them / 2.1：

Dihedral Angle PCA Allows Us to Separate Internal and Global Motion / 2.2：

Dimensionality of the Free Energy Landscape / 2.3：

Characterization of the Free Energy Landscape: States, Barriers, and Transitions / 2.4：

Low-Dimensional Simulation of Biomolecular Dynamics to Catch Slow and Rare Processes / 2.5：

PCA by Parts: The Folding Pathways of Villin Headpiece / 2.6：

The Energy Landscape of Aggregating Aβ-Peptides / 2.7：

Concluding Remarks / 2.8：

Local Backbone Preferences and Nearest-Neighbor Effects in the Unfolded and Native States / Joe DeBaitolo ; Abhishek Jha ; Karl F. Freed ; Tobin R. Sosnick3：

Early Days: Random Coil-Theory and Experiment / 3.1：

Denatured Proteins as Self-Avoiding Random Coils / 3.3：

Modeling the Unfolded State / 3.4：

NN Effects in Protein Structure Prediction / 3.5：

Utilizing Folding Pathways for Structure Prediction / 3.6：

Native State Modeling / 3.7：

Secondary-Structure Propensities: Native Backbones in Unfolded Proteins / 3.8：

Conclusions / 3.9：

Short-Distance FRET Applied to the Polypeptide Chain / Maik H. Jacob ; Werner M. Nau4：

A Short Timeline of Resonance Energy Transfer Applied to the Polypeptide Chain / 4.1：

A Short Theory of FRET Applied to the Polypeptide Chain / 4.2：

DBO and Dbo / 4.3：

Short-Distance FRET Applied to the Structured Polypeptide Chain / 4.4：

Short-Distance FRET to Monitor Chain-Structural Transitions upon Phosphorylation / 4.5：

Short-Distance FRET Applied to the Structureless Chain / 4.6：

The Future of Short-Distance FRET / 4.7：

Dedication

Solvation and Electrostatics as Determinants of Local Structural Order in Unfolded Peptides and Proteins / Franc Avbelj5：

Local Structural Order in Unfolded Peptides and Proteins / 5.1：

ESM / 5.2：

The ESM and Strand-Coil Transition Model / 5.3：

The ESM and Backbone Conformational Preferences / 5.4：

The Nearest-Neighbor Effect / 5.5：

The ESM and Cooperative Local Structures-Fluctuating β-Strands / 5.6：

The ESM and β-Sheet Preferences in Native Proteins- Significance of Unfolded State / 5.7：

The ESM and Secondary Chemical Shifts of Polypeptides / 5.8：

Role of Backbone Solvation in Determining Hydrogen Exchange Rates of Unfolded Polypeptides / 5.9：

Other Theoretical Models of Unfolded Polypeptides, 148 Acknowledgments / 5.10：

Experimental and Computational Studies of Polyproline II Propensity / W. Austin Elam ; Travis P. Schrank ; Vincent J. Hilser6：

Experimental Measurement of PII Propensities / 6.1：

Computational Studies of Denatured State Conformational Propensities / 6.3：

A Steric Model Reveals Common PII Propensity of the Peptide Backbone / 6.4：

Correlation of PII Propensity to Amino Acid Properties / 6.5：

Summary / 6.6：

Mapping Conformational Dynamics in Unfolded Polypeptide Chains Using Short Model Peptides by NMR Spectroscopy / Daniel Mathieu ; Karin Rybka ; Jürgen Graf ; Harald Schwalbe7：

General Aspects of NMR Spectroscopy / 7.1：

NMR Parameters and Their Measurement / 7.3：

Translating NMR Parameters to Structural Information / 7.4：

Secondary Structure and Dynamics of a Family of Disordered Proteins / Pranesh Narayanaswami ; Gaiy W. Daughdrill7.5：

Materials and Methods / 8.1：

Results and Discussion / 8.3：

Disordered Peptides and Molecular Recognition / II：

Binding Promiscuity of Unfolded Peptides / Christopher J. Oldfield ; Bin Xue9：

Protein-Protein Interaction Networks / 9.1：

Role of Intrinsic Disorder in PPI Networks / 9.2：

Transient Structural Elements in Protein-Based Recognition / 9.3：

Chameleons and Adaptors: Binding Promiscuity of Unfolded Peptides / 9.4：

Principles of Using the Unfolded Protein Regions for Binding / 9.5：

Intrinsic Flexibility of Nucleic Acid Chaperone Proteins from Pathogenic RNA Viruses / Roland Ivanyi-Nagy ; Zuzanna Makowska ; Jean-Luc Darlix9.6：

Retroviruses and Retroviral Nucleocapsid Proteins / 10.1：

Core Proteins in the Flaviviridae Family of Viruses / 10.3：

Coronavirus Nucleocapsid Protein / 10.4：

Hantavirus Nucleocapsid Protein / 10.5：

Aggregation of Disordered Peptides / III：

Self-Assembling Alanine-Rich Peptides of Biomedical and Biotechnological Relevance / Thomas J. Measey ; Reinhard Schweitzer-Stenner11：

Biomolecular Self-Assembly / 11.1：

Misfolding and Human Disease / 11.2：

Exploitation of Peptide Self-Assembly for Biotechnological Applications / 11.3：

Structural Elements Regulating Interactions in the Early Stages of Fibrillogenesis: A Human Calcitonin Model System / Rosa Maria Vitale ; Giuseppina Andreotti ; Pietro Amodeo ; Andrea Motta11.4：

Stating the Problem / 12.1：

Aggregation Models: The State of The Art / 12.2：

Human Calcitonin hCT as a Model System for Self-Assembly / 12.3：

The "Prefibrillar" State of hCT / 12.4：

How Many Molecules for the Critical Nucleus? / 12.5：

Modeling Prefibrillar Aggregates / 12.6：

hCT Helical Oligomers / 12.7：

The Role of Aromatic Residues in the Early Stages of Amyloid Formation / 12.8：

The Folding of hCT before Aggregation / 12.9：

Model Explains the Differences in Aggregation Properties between hCT and sCT / 12.10：

hCT Fibril Maturation / 12.11：

α-Helix →β-Sheet Conformational Transition and hCT Fibrillation / 12.12：

Solution NMR Studies of Aβ Monomers and Oligomers / Chunyu Wang12.13：

Overexpression and Purification of Recombinant Aβ / 13.1：

Aβ Monomers / 13.3：

Aβ Oligomers and Monomer-Oligomer Interaction / 13.4：

Conclusion / 13.5：

Thermodynamic and Kinetic Models for Aggregation of Intrinsically Disordered Proteins / Scott L. Crick ; Rohit V. Pappu14：

Thermodynamics of Protein Aggregation-the Phase Diagram Approach / 14.1：

Thermodynamics of IDP Aggregation (Phase Separation)- MPM Description / 14.3：

Kinetics of Homogeneous Nucleation and Elongation Using MPMs / 14.4：

Concepts from Colloidal Science / 14.5：

Modifiers of Protein Aggregation-From Nonspecific to Specific Interactions / Michal Levy-Sakin ; Roni Scherzer-Attali ; Ehud Gazit14.6：

Nonspecific Modifiers / 15.1：

Specific Modifiers / 15.3：

Computational Studies of Folding and Assembly of Amyloidogenic Proteins / J. Srinivasa Rao ; Brigita Urbane ; Luis Cniz16：

Amyloids / 16.1：

Computer Simulations / 16.3：

Index / 16.4：

Introduction to the Wiley Series on Protein and Peptide Science

Preface

Contributors

Introduction

Why Are We Interested in the Unfolded Peptides and Proteins? / Vladimir N. Uversky ; A. Keith Dunker1：

Why Study IDPs? / 1.1：

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